In the year 23XX, turmoil reigns. The champion of humanity, Mega Man X, has become a despotic ruler over the nation of Neo Arcadia. Those who dare to speak out against his reign are silenced.

The Resistance, an organization devoted ending X's tyranny, has made a discovery. An ancient ruin, surviving the devastation of X's reign, contains a vault which holds a solitary Reploid in stasis. All indications are that this is Zero, X's former ally.

Zero has been awakened, and has agreed to help the Resistance in their time of need, and bring X to justice. Will the return of this centuries-old Reploid mean the end of an empire, or further solidify its hold on the world?